Contacts of the helix formed by residues 227 - 238 (chain B) in PDB entry 5I2Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 3.0 29.6 + - - -
151B HIS* 4.0 20.1 + - + +
223B GLY 4.2 1.2 + - - -
224B CYS 3.4 13.2 + - - +
225B ASN 3.3 1.4 - - - -
226B GLN* 1.3 79.1 - - - +
228B LEU* 1.3 54.4 + - - +
229B ASP* 2.9 35.3 + - - +
230B VAL* 3.0 18.9 + - + +
231B GLN* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLN 4.2 9.2 - - - +
227B ASP* 1.3 73.2 + - - +
229B ASP* 1.3 64.1 + - - +
231B GLN* 3.7 23.6 - - + +
232B LYS* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 3.0 25.2 + - - -
104B LEU* 3.3 30.8 - - + +
227B ASP* 2.9 15.0 + - - +
228B LEU* 1.3 77.4 - - - +
230B VAL* 1.3 62.0 + - - +
232B LYS* 3.5 4.9 + - - +
233B LYS* 3.2 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 4.0 19.3 - - + -
103B ILE* 4.0 20.9 - - + -
104B LEU* 4.0 13.0 - - + -
202B PHE* 3.6 26.3 - - + -
224B CYS 3.3 30.1 - - - +
225B ASN* 4.3 8.5 - - - +
227B ASP* 3.0 21.7 + - + +
229B ASP* 1.3 75.9 - - - +
231B GLN* 1.3 60.7 - - - +
233B LYS* 3.3 3.2 + - - +
234B LEU* 2.9 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ASN 2.9 28.4 + - - +
226B GLN* 3.9 15.2 + - - +
227B ASP 2.8 14.8 + - - +
228B LEU* 3.7 21.9 - - + +
230B VAL* 1.3 76.7 - - - +
232B LYS* 1.3 62.1 + - - +
234B LEU* 3.3 10.4 + - + +
235B TYR* 3.1 46.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU 2.9 19.0 + - - +
229B ASP* 3.8 6.7 - - - +
230B VAL 3.3 0.4 - - - -
231B GLN* 1.3 75.2 - - - +
233B LYS* 1.3 63.1 + - - +
235B TYR* 3.2 8.4 + - - +
236B ASP* 3.1 41.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE 3.7 20.4 + - - +
104B LEU* 3.1 36.8 + - + +
105B GLY 4.3 0.2 + - - -
106B SER* 3.8 23.4 - - - +
202B PHE* 4.1 15.0 - - + -
229B ASP 3.2 15.5 + - - +
230B VAL* 3.7 4.0 - - - +
232B LYS* 1.3 76.2 - - - +
234B LEU* 1.3 66.4 + - - +
236B ASP* 3.0 23.7 + - + +
237B CYS* 3.1 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.0 28.5 - - + -
200B ALA* 3.2 35.2 - - + +
201B GLU* 4.3 7.9 - - - +
202B PHE* 3.5 28.2 - - + -
225B ASN* 4.4 9.4 - - + +
230B VAL 2.9 14.6 + - - +
231B GLN* 3.3 14.6 + - + +
233B LYS* 1.3 74.3 - - - +
235B TYR* 1.3 74.9 + - + +
237B CYS* 3.2 5.0 + - + +
238B LEU* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PRO* 3.8 25.3 - - + +
200B ALA* 4.9 1.7 + - + -
231B GLN* 3.1 41.4 + - + +
232B LYS* 3.2 7.2 + - + +
234B LEU* 1.3 89.2 - - + +
236B ASP* 1.3 62.1 + - - +
238B LEU* 3.8 30.3 - - + +
239B GLU* 2.9 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LYS* 3.1 33.5 + - - +
233B LYS* 3.0 17.1 + - + +
235B TYR* 1.3 80.0 - - - +
237B CYS* 1.3 65.7 + - - +
238B LEU 3.4 0.2 - - - -
239B GLU* 3.4 12.6 + - - +
240B GLU* 3.5 27.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.9 14.4 - - + -
202B PHE* 4.3 18.4 - - - -
233B LYS* 3.1 30.9 + - - -
234B LEU* 3.2 8.9 + - - +
236B ASP* 1.3 79.7 - - - +
238B LEU* 1.3 64.2 + - + +
240B GLU* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.2 22.0 - - + -
193B VAL* 4.7 15.3 - - + -
200B ALA* 3.9 22.9 - - + +
234B LEU* 3.1 16.8 + - + +
235B TYR* 3.8 35.4 - - + +
236B ASP 3.4 0.4 - - - -
237B CYS* 1.3 77.6 - - + +
239B GLU* 1.3 61.5 + - + +
240B GLU 3.1 7.9 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il